Thermo Fisher Scientific UVPD Module User guide

Type
User guide
UVPD Module
User Guide
For the Orbitrap Fusion Lumos Tribrid Mass Spectrometer
80011-97502 Revision A July 2017
© 2017 Thermo Fisher Scientific Inc. All rights reserved.
Fusion and Lumos are trademarks, and Orbitrap, Orbitrap Fusion, Orbitrap Fusion Lumos, Thermo
Scientific, Tribrid, and Xcalibur are registered trademarks of Thermo Fisher Scientific Inc. in the United States.
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registered trademarks of Microsoft Corporation.
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Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
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document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.
Release history: Rev A, July 2017
Software version: (Thermo) Foundation 3.1 SP4 and later, Xcalibur 4.1 and later, Tune 3.0 and later
For Research Use Only. Not for use in diagnostic procedures.
Regulatory Compliance
Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with
applicable North American and European regulations. Your system meets the applicable requirements in the
electromagnetic compatibility (EMC) and product safety standards described in this section.
Changes that you make to your system might void compliance with one or more of these regulatory standards. Changes
to your system include replacing a part or adding components, options, or peripherals not specifically authorized and
qualified by Thermo Fisher Scientific. To ensure continued compliance with the regulatory standards, order
replacement parts and additional components, options, and peripherals directly from Thermo Fisher Scientific or an
authorized representative.
Laser product safety
This device complies with the FDA Class 1 requirements in 21 CFR 1040.10. It also complies with the laser safety
standards IEC 60825-1: 2017 and ANSI Z316.1-2014.
Low Voltage Directive 2014/35/EU
This device complies with Low Voltage Directive 2014/35/EU and the harmonized safety standard IEC/EN/CSA/
UL 61010-1, 3rd Edition.
EMC Directive 2014/30/EU and other EMC test standards
This device was tested by TÜV Rheinland of North America and complies with the following EMC standards:
47 CFR 15, Subpart B, Class A: 2015 VCCI V-3/2015.04 IEC/EN 61000-4-4: 2004 + A1
AS/NZS CISPR 22: 2009 EN 55011: 2009 + A1 IEC/EN 61000-4-5: 2006
BSMI CNS 13438: 2006 IEC/EN 61326-1: 2013 IEC/EN 61000-4-6: 2009
ICES-003: 2014 IEC/EN 61000-3-2: 2006 + A1 + A2 IEC/EN 61000-4-8: 2010
IEC/CISPR 11: 2009 + A1 IEC/EN 61000-3-3: 2008 IEC/EN 61000-4-11: 2004
KN 61000-6-2 IEC/EN 61000-4-2: 2009
KN 61000-6-4 IEC/EN 61000-4-3: 2006 + A1 + A2
FCC Compliance Statement
Notice on the Proper Use of
Thermo Scientific Instruments
In compliance with international regulations: This instrument must be used in the manner specified by Thermo Fisher
Scientific to ensure protections provided by the instrument are not impaired. Deviations from specified instructions on
the proper use of the instrument include changes to the system and part replacement. Accordingly, order replacement
parts from Thermo Fisher Scientific or one of its authorized representatives.
THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO
THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL
INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED,
INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.
CAUTION Read and understand the various precautionary notes, signs, and symbols contained inside
this manual pertaining to the safe use and operation of this product before using the device.
Thermo Scientific UVPD Module User Guide v
C
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Accessing Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
Special Notices, Symbols, and Cautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Ultraviolet Photodissociation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
UVPD Scan Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
UVPD Readback Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Chapter 2 UVPD Module. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Laser Module. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Controller Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Chapter 3 UVPD Laser Beam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Laser Alignment Quality Score . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Laser Beam Movement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Laser Beam Overlap with the Ion Clouds in the Ion Trap Chamber . . . . . . . . . 12
Chapter 4 UVPD Calibration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Laser Alignment Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Precursor Decay Rate Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Laser Alignment Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Running the UVPD Calibration Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Manually Aligning the Laser Beam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Chapter 5 UVPD Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25
Setting Up the MS/UVPD System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Optimizing the API Source Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Defining the Scan Parameters for the Experiment . . . . . . . . . . . . . . . . . . . . . . . 30
Acquiring Sample Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Contents
Contents
vi UVPD Module User Guide Thermo Scientific
Appendix A Laser Safety Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Laser Safety Cautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Laser Safety Labels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Laser Head Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
Thermo Scientific UVPD Module User Guide vii
F
Figure 1. Approximate location of the UVPD laser module inside the Orbitrap Fusion
Lumos MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Figure 2. UVPD scan parameters in the Tune application . . . . . . . . . . . . . . . . . . . . . . . . . 3
Figure 3. Laser module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Figure 4. Complementary pairs of micrometers (front view) . . . . . . . . . . . . . . . . . . . . . . . . 7
Figure 5. Mirror assemblies behind the laser beam protective housing . . . . . . . . . . . . . . . . 7
Figure 6. Micrometer locking thumbscrew and graduation markings . . . . . . . . . . . . . . . . . 8
Figure 7. Controller module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Figure 8. Example of optimal UVPD efficiency and AQS . . . . . . . . . . . . . . . . . . . . . . . . . 10
Figure 9. Laser beam paths after adjusting one or more micrometers . . . . . . . . . . . . . . . . 11
Figure 10. Laser beam (blue) overlap with an ion cloud (green) in the ion trap . . . . . . . . . . 12
Figure 11. Examples of optimal and poor UVPD efficiency (level laser beam through
the trap) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Figure 12. Examples of optimal and poor UVPD efficiency (angled laser beam through
the trap) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Figure 13. Laser Alignment calibration displays (percentage of precursor fragmentation
and AQS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Figure 14. Plot of the precursor decay rate in the ion trap’s low-pressure cell . . . . . . . . . . . 17
Figure 15. Plot of the UVPD reaction time for the caffeine precursor . . . . . . . . . . . . . . . . . 17
Figure 16. Plot of the UVPD alignment quality check . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Figure 17. Plot of the UVPD fragmentation efficiency check . . . . . . . . . . . . . . . . . . . . . . . 18
Figure 18. UVPD check calibration procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Figure 19. UVPD calibration procedures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Figure 20. Laser module compartment with door removed . . . . . . . . . . . . . . . . . . . . . . . . 21
Figure 21. Syringe pump settings box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Figure 22. Define Scan pane showing the scan parameters for optimizing the ion source. . . 27
Figure 23. RSD results for spray stability when optimizing the ion source parameters . . . . 28
Figure 24. Full MS scan spectrum of the enfuvirtide solution (profile mode) . . . . . . . . . . . 29
Figure 25. Define Scan pane showing the scan parameters for the UVPD experiment . . . . 30
Figure 26. MS2 scan spectrum of the enfuvirtide solution (profile mode) . . . . . . . . . . . . . . 31
Figure 27. Location of the laser safety label on the Orbitrap Fusion Lumos MS with the
UVPD option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Figure 28. Laser safety label for the Orbitrap Fusion Lumos MS with the UVPD option . . 34
Figure 29. Internal laser safety label (on and behind the laser beam protective housing) . . . 35
Figure 30. Laser head’s Class 4 laser safety label . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Figures
Figures
viii UVPD Module User Guide Thermo Scientific
Thermo Scientific UVPD Module User Guide ix
P
Preface
The UVPD Module User Guide describes the primary components for the optional Thermo
Scientific™ ultraviolet photodissociation (UVPD) hardware module installed in the Thermo
Scientific Orbitrap Fusion Lumos™ (also known as Lumos™) Tribrid™ mass spectrometer
(MS). It also provides an example experiment and instructions for calibrating the alignment of
the invisible laser beam.
Contents
Accessing Documentation
Special Notices, Symbols, and Cautions
•Contacting Us
To suggest changes to the documentation or to the Help
Complete a brief survey about this document by clicking the button below.
Thank you in advance for your help.
Accessing Documentation
The Orbitrap Fusion Lumos MS includes complete documentation. For system requirements,
refer to the release notes on the software DVD.
To view the product manuals
From the Microsoft™ Windows™ taskbar, choose Start > All Programs > Thermo
Instruments > model x.x, and then open the applicable PDF file.
Preface
xUVPD Module User Guide Thermo Scientific
To view Help
Do the following as applicable:
Thermo Tune instrument-control software: Click the Options icon, , and
choose Tu n e He l p .
Thermo Xcalibur™ Method Editor: Choose an option from the Help menu (or press
the F1 key).
To view user documentation from the Thermo Fisher Scientific website
1. Go to thermofisher.com.
2. Point to Services & Support and click Manuals on the left.
3. In the Refine Your Search box, search by the product name.
4. From the results list, click the title to open the document in your web browser, save it, or
print it.
To return to the document list, click the browser Back button.
Special Notices, Symbols, and Cautions
Make sure you understand the special notices, symbols, and caution labels in this guide. Most
of the special notices and cautions appear in boxes; those pertaining to safety also have
corresponding symbols. Some symbols are also marked on the instrument itself and can
appear in color or in black and white. For complete definitions, see Table 1.
Table 1. Notices, symbols, labels, and their meanings (Sheet 1 of 2)
Notice, symbol, or label Meaning
IMPORTANT Highlights information necessary to prevent damage to
software, loss of data, or invalid test results; or might contain
information that is critical for optimal performance of the
product.
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.
Preface
Thermo Scientific UVPD Module User Guide xi
Caution: Read the cautionary information associated with this
task.
Chemical hazard: Observe safe laboratory practices and
procedures when handling chemicals. Only work with volatile
chemicals under a fume or exhaust hood. Wear gloves and other
protective equipment, as appropriate, when handling toxic,
carcinogenic, mutagenic, corrosive, or irritant chemicals. Use
approved containers and proper procedures to dispose of waste
oil and when handling wetted parts of the instrument.
Heavy object: The Orbitrap Fusion Series MS, excluding its
workbench, weighs over 227 kg (500 lb). Never try to detach
and move the instrument from its workbench; you can suffer
personal injury or damage the instrument.
Hot surface: Allow any heated components to cool before
touching them.
Risk of electric shock: This instrument uses voltages that can
cause electric shock and personal injury. Before servicing the
instrument, shut it down and disconnect it from line power.
While operating the instrument, keep covers on.
Risk of eye injury: Eye injury can occur from splattered
chemicals, airborne particles, or sharp objects. Wear safety
glasses when handling chemicals or servicing the instrument.
Risk of laser radiation: Failure to understand and comply with
laser cautions and operating instructions in this guide can result
in property damage or serious injuries to the user.
Sharp object: Avoid handling the tip of the syringe needle.
Table 1. Notices, symbols, labels, and their meanings (Sheet 2 of 2)
Notice, symbol, or label Meaning
Preface
xii UVPD Module User Guide Thermo Scientific
Contacting Us
Contact Email Telephone QR Codea
aYou can use your smartphone to scan a QR Code, which opens your email application or browser.
U.S. Technical Support us.techsupport.analyze@thermofisher.com (U.S.) 1 (800) 532-4752
U.S. Customer Service
and Sales
us.customer-support.analyze@thermofisher.com (U.S.) 1 (800) 532-4752
Global support To find global contact information or customize your request
1. Go to thermofisher.com.
2. Click Contact Us, select the country, and then select the type of support
you need.
3. At the prompt, type the product name.
4. Use the phone number or complete the online form.
To find product support, knowledge bases, and resources
Go to thermofisher.com/us/en/home/technical-resources.
To find product information
Go to thermofisher.com/us/en/home/brands/thermo-scientific.
Note To provide feedback for this document, go to surveymonkey.com/s/PQM6P62 or send an email message to
Technical Publications (techpubs-lcms@thermofisher.com).
Thermo Scientific UVPD Module User Guide 1
1
Introduction
The Orbitrap Fusion Lumos Tribrid MS is a member of the Thermo Scientific family of mass
spectrometers. The optional UVPD module assembly can come factory-installed with the
purchase of the Orbitrap Fusion Lumos MS, or a laser-safety-trained Thermo Fisher Scientific
field service engineer can install it at a later date as an upgrade.
An Orbitrap Fusion Lumos MS with UVPD capability incorporates an assembly consisting of
a laser module and a control module, both of which are located inside the instrument. For
information about these modules, see Chapter 2, “UVPD Module.For information about
the invisible laser beam, see Chapter 3, “UVPD Laser Beam.For laser safety information, see
Appendix A, “Laser Safety Information.
For procedures regarding daily operation, maintenance, and system startup and shutdown,
refer to the Orbitrap Fusion Series Hardware Manual.
Contents
Ultraviolet Photodissociation
UVPD Scan Parameters
UVPD Readback Measurements
Note The UVPD option is not available for the Thermo Scientific Orbitrap Fusion™ (also
known as Fusion™) Tribrid MS.
CAUTION Use of controls or adjustments or performance of procedures other than those
specified herein may result in hazardous radiation exposure.
Note The Glossary defines some of the terms used in this manual.
1 Introduction
Ultraviolet Photodissociation
2UVPD Module User Guide Thermo Scientific
Ultraviolet Photodissociation
The Orbitrap Fusion Lumos MS with UVPD capability incorporates an internal UVPD
module, which is located behind the right-side panel that connects to the ion trap chamber
manifold. Inside the module, a compact, solid-state laser head (CryLaS GmbH) generates a
pulsed 213 nm invisible laser beam that enters the ion trap, irradiating ions and producing
fragment ions. While collision-induced dissociation (CID) uses a vibrational excitation
mechanism to fragment molecular ions, UVPD uses an electronic excitation mechanism to
induce fragmentation.
Figure 1. Approximate location of the UVPD laser module inside the Orbitrap Fusion Lumos MS
As a fragmentation technique, UVPD offers several advantages:
More informative fragmentation for a wide variety of compounds.
More complete sequence coverage for intact proteins as well as unique structural
information for small molecules.
Fast and direct cleavage of amide bonds at 5.82 eV per photon.
Not limited by the precursor charge state, unlike ETD fragmentation.
A wider array of sequence fragment types (a/x, b/y, and c/z) when activating peptidic
precursors.
Simplicity. Activation time is the only parameter, which the MS sets automatically based
on the precursor molecular weight during method runs when the MS can determine the
precursors charge state.
UVPD compartment door
Laser Module
1 Introduction
UVPD Scan Parameters
Thermo Scientific UVPD Module User Guide 3
UVPD Scan Parameters
When you select the MS2 or MSn scan type in the Thermo Scientific Tune applications
Define Scan pane (Figure 2), you can then select UVPD as the Activation Type and set the
UVPD activation time (in milliseconds). When you create a method in the Method Editor
application, you also have the option of using the molecular-weight-based UVPD activation
time that is determined by the Precursor Decay Rate Calibration.
For instructions on how to acquire data by using the Tune application, refer to the Orbitrap
Fusion Series Getting Started Guide. For descriptions of the parameters in the Define Scan
pane, refer to the Orbitrap Fusion Lumos Tune Help.
Figure 2. UVPD scan parameters in the Tune application
UVPD Readback Measurements
In addition to monitoring the overall system readback status in the Tune application, you can
monitor individual UVPD readback values on the By Board and By Function pages of the
Status pane. Table 2 lists the defaults for the UVPD readback values.
UVPD activation type
Table 2. Default values for the UVPD readbacks
Readback Typical value
Laser Status Ready, Standby, Not Connected
Laser On, Off
Laser Diode Voltage 1–6 V
Laser Temperaturea
aBy Board page only
10–60 °C
Laser Total Hoursa(Number of laser power-on hours)
Laser Pulse Counta0–500 Gigashots
1 Introduction
UVPD Readback Measurements
4UVPD Module User Guide Thermo Scientific
Thermo Scientific UVPD Module User Guide 5
2
UVPD Module
The UVPD module assembly for the Orbitrap Fusion Lumos MS has two principal
components—the laser module and the controller module. Installation of these modules
includes connections to three of the instrument printed circuit boards (PCBs):
Carrier PCB—Provides USB communication between the MS and the laser controller.
Distribution PCB—Powers the laser module.
Source PCB—Provides the laser trigger signal during the UVPD scan functions.
Contents
•Laser Module
Controller Module
Laser Module
The laser module (Figure 3) is located inside the MS on the right side. The user-accessible
laser compartment is behind the removable side door. The laser module assembly includes a
213 nm laser head, two adjustable mirror assemblies (each with two micrometers), and an
interlock switch assembly.
Note You cannot service the PCBs. If you need assistance, contact Thermo Fisher
Scientific Technical Support.
CAUTION Do not remove the laser beam protective housing. The protective housing
and safety interlock system prevent access to the invisible Class 4 laser beam. Exposure to
the beam can cause serious skin and eye injuries, including blindness.
2 UVPD Module
Laser Module
6UVPD Module User Guide Thermo Scientific
Figure 3. Laser module
Adjacent to each micrometer is a numbered label (1 to 4). Figure 4 shows the numbering and
the assigned “complementary pairs” of micrometers, which are 1-2 (top micrometers) and 3-4
(bottom micrometers). Complementary pairs work in the same plane of motion—that is,
movement that is vertical (pair 1-2) or horizontal (pair 3-4).
Protective housing
(shown as blue and
gold)
Mirror 2 (M2) assembly
(micrometers # 2 and #4)
Laser head with Class 4 laser safety labels
in yellow (see Figure 30 for label contents)
Mirror 1 (M1) assembly (micrometers #1 and #3)
Protective housing with Class 4 laser safety
label (see Figure 29 for label contents)
Label to record the fine-alignment micrometer positions
1
4
3
2
Interlock switch assembly (not shown)
2 UVPD Module
Laser Module
Thermo Scientific UVPD Module User Guide 7
Figure 4. Complementary pairs of micrometers (front view)
Figure 5 shows the mirror assemblies behind the protective housing. Each mirror assembly has
two micrometers that control the position of its mirror.
Figure 5. Mirror assemblies behind the laser beam protective housing
Top micrometers: pair 1–2
Bottom micrometers: pair 3–4
Micrometer number
4
2
3
1
Class 4 laser safety label (see Figure 29 for label contents)
M1 assembly Laser window into
the ion traps
M2 assembly
Interlock switch assembly
4
2
Laser head
1
3
2 UVPD Module
Controller Module
8UVPD Module User Guide Thermo Scientific
Figure 6 shows the micrometer and defines the graduation markings on its sleeve and thimble.
Figure 6. Micrometer locking thumbscrew and graduation markings
Controller Module
The controller module (Figure 7) is located inside the MS behind the back panel near the
distribution PCB. Enclosed within the controller module assembly is a power supply and a
controller unit, which controls the laser head.
Figure 7. Controller module
Thimble: Each mark is 0.005 mm (5 μm).Thumbscrew lock
Sleeve: Each top mark is 1 mm, and each bottom mark shows
half-millimeter positions (for example, 0.5 and 1.5 mm).
(End of 12 Vdc output cord
not shown)
Laser remote interlock connector
Controller unit (12 Vdc input)
Power supply (220 Vac input)
Laser head interface connector
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